GROMACS Tutorial

Virtual Sites

Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry

This example will guide a new user through the process of building a linear molecule using virtual sites. The tutorial assumes the user is familiar with basic GROMACS workflows and topology organization.

This tutorial assumes you are using GROMACS version in the 2018.x series. While some older versions may work, pre-4.5 versions of GROMACS will not work with the example shown here due to changes to the topology format and nomenclature.

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